UVS Fish Codes

This table maps shorthand taxon codes used during underwater visual surveys (UVS) to authoritative taxonomic identifiers and names. It serves as a translation layer between diver-entered field codes and the canonical taxonomy in taxonomy.fish.

Each row corresponds to a unique taxon_code used in the field, whether referring to an accepted species, a synonym, or a higher-level taxon (genus or family). This mapping enables consistent, traceable integration of UVS data with modern taxonomic standards and trait metadata.

Why it matters

• Legacy harmonization: Links historical field entries to accepted names and identifiers
• Soft joins: Enables flexible, code-to-species mapping across datasets
• Traceability: Maintains original diver intent while supporting global taxonomy

This table captures both the field-level identity (what divers recorded) and the accepted scientific classification (based on WoRMS and FishBase), enabling robust reconciliation and trait-based analysis.

Table 1: UVS Fish Codes

Field	Type	Required	Description
taxon_code	STRING	true	Short code used in field datasheets (e.g., CH.ATR)
taxon_name	STRING	true	Original name assigned to code (e.g., Chromis atrilobata)
aphia_id	INTEGER	true	AphiaID corresponding to taxon_name (may be outdated or unaccepted)
rank	STRING	true	Taxonomic rank of the observation (species, genus, family)
status	STRING	true	Taxonomic status of original name (accepted, synonym, unresolved)
accepted_name	STRING	true	Accepted scientific name (Genus species)
accepted_aphia_id	INTEGER	true	Accepted AphiaID for current taxonomy
fb_spec_code	INTEGER	false	Optional FishBase SpecCode for cross-referencing
notes	STRING	false	Optional comments or notes (e.g., name updates, uncertainty)

How are codes generated?

taxon_code is the primary join key across all UVS fish datasets in the Pristine Seas Database. These short, deterministic codes are optimized for diver entry — concise, unambiguous, and easy to write underwater.

Taxon Code Logic

Field codes (taxon_code) are used across UVS datasets to record species in a compact, consistent format optimized for field entry. They follow a structured and deterministic convention:

Format for Species-Level Codes

GEN2.SPEC4 — First 2 letters of the genus + first 4 of the species (uppercase)

• Acanthurus tristis → AC.TRIS
  
• Apogon tricolor → AP.TRIC
  
• Anthias tricolor → AN.TRIC

Handling Duplicates

When multiple species would share the same code:

• The most common taxon keeps the default
• Others extend the genus or species portion to ensure uniqueness

Examples
- Apogon tristis → AP.TRIS
- Aplodactylus tristis → APL.TRIS
- Labroides bilineatus → LA.BILI
- Labroides bilinearis → LA.BILIN

Genus- and Family-Level Codes

Used when IDs are not to species:

• Genus → GEN4.SP (e.g., Labroides sp. → LABR.SP)
  
• Family → FAM4.SPP (e.g., Labridae spp. → LABR.SPP)

These conventions ensure clean joins, traceability, and consistent taxonomy across field data and reference tables.